ROUGH IDLE

2002 Toyota Corolla • 187,000 miles

I have a toyota corolla with a rough idle that really has me stumped. If you have any ideas I am surely open to them, this rough idle only occurrs when the car is put in gear the first time after the car starts up( which just purrs). After about 3-4 min. When putting the car in gear it operates very smoothly, this lead me to think that something is blocked either partially or completetly. I have cleaned or replaced every filter I can think of except the MAF. I think this may be the issue, but where is it located?
As I said previously any ideas would be greatly appreciated.